Hello, I want to know how many genomes there are of a specific genus in genbank, for example Enterobacter. Where do I have to look for? in assembly or in genome?
http://www.ncbi.nlm.nih.gov/gquery/?term=enterobacter
Thanks.
Assembly summary file is very informative. If the 8th field of said field begins like "Enterobacter<space>"..
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt
awk 'BEGIN{FS="\t"; count=0}{if($8~/^Enterobacter /){count++}}END{print count}' assembly_summary_genbank.txt
1103
Thanks for the answer!! Why the result of the script (1103) is different from the number that appears in assembly in this page(1136) ? http://www.ncbi.nlm.nih.gov/gquery/?term=enterobacter
If you follow the assembly link it says on top:
Items: 1 to 20 of 1105
Filters activated: Latest, Exclude anomalous. Clear all to show 1136 items.
The assembly summary file only includes the latest assembly versions. The awk command for the latest assembly summary file returns 1104 hits so it lags a little bit behind entrez (I imagine because they don't update the file every second).
Log in to answer this question.
